Okay, I have it narrowed down to these two. I would eventually like to put my equipment in a closet. I figure it would cost about the same to get a One with a Hot link Pro setup or a 890 Pro with the RF link.
Can someone recommend one over the other? Are there any features one has that the other doesn't? Tell me which to buy and I'll be happy, it hurts my brain. :)

I have the One with an IR extender and it works great. Other than the remote itself, which is really personal preference, here are the pros and cons:

890 pro - don't have to aim the remote at the IR sensor and you can individually address duplicate components - IOW if you have 2 of the same device and the device doesn't support multiple remote addresses you can have the RF extender send a command directly to each device independently via dedicated emitters.

One with IR extender - here is the BIG advantage IN MY OPINION: you can not only use the One but you can use ANY IR universal remote from Harmony or anyone else and you can use the OEM remotes at any time.

I use a Niles setup with a wall mounted receiver, a controller and one flood emitter to control a receiver, PS3 and DirecTV DVR in one rack in the closet. Works great. You can also get ceiling mounted receivers and mini receivers that you can mount in a cabinet face frame. This is more flexible and allows you to mix and match the emitters and receivers and allows longer cable runs than the hot link pro, but probably costs a bit more.

The big difference would me relates to how many programmable buttons/screen you need. DirecTV requires Red, Yellow, Blue & Green buttons...neither the One or 890 has it...but the 890 has space for eight buttons on each LCD screen, while I think the One is limited to three.

The One has six buttons on the LCD screen.
Devices with colour buttons initially have them allocated to the screen.
Most Activities initially leave unused hard buttons that can be customised for any other commands.
The colours are actually more practical when customised to a convenient group of spare hard buttons, and the screen is usually left to show the Activities rather than commands.

Any other pointers or comparison?

You did not mention controlling lighting, but the 890 PRO will control Z-wave controllers.

890 = single room setting (simple Web Interface for setup)
890 Pro = Multi room settings (More Complex Web Interface for setup)

In addition, the 890 is the only Logitech Harmony remote that will do z-wave scene control.

I picked up a 890 Pro, spent an hour on the phone with Harmony RF support to work out the bugs and am pretty happy with the overall.

I believe the 890 will not do custom icons but know the Harmony One will (channel icons and such)

If your devices are all line of sight, don't mind pointing the remote and do not plan Z-wave control then the One is a better choice.